Permission Denied Error While Using Quake

Question

[Medhat]

I installed Quake following this tutorial Here I installed Jellyfish and boost under /usr/local also R and VGAM package are installed

when I use this command

python quake.py -f /home/medhat/Downloads/genomeList.ls -k 15 -p 2

to use the Quake program it gives me this error

Guessing quality values are on ascii 33 scale
/bin/sh: 1: /home/medhat/source/Quake/bin/jellyfish: Permission denied
/bin/sh: 1: /home/medhat/source/Quake/bin/jellyfish: Permission denied
 Traceback (most recent call last):
 File "quake.py", line 324, in <module>
  main()
 File "quake.py", line 89, in main
  jellyfish(options.readsf, options.reads_listf, options.k, ctsf, quality_scale, options.hash_size, options.proc)
 File "quake.py", line 290, in jellyfish
  os.rename('%s.dbm_0' % output_pre, '%s.dbm' % output_pre)

OSError: [Errno 2] No such file or directory

I used chmod to change permission of the jellyfish director but nothing happened

also I used sudo befor the command "python quake.py -f /home/medhat/Downloads/genomeList.ls -k 15 -p 2" but nothing change lastly the content of the "/home/medhat/Downloads/genomeList.ls" file is path to fastq file /home/medhat/Downloads/frag_1.fastq

Thanks for help

[Devon Ryan]

You mentioned changing permission on /home/medhat/source/Quake/bin, but have you also checked the permissions on /home/medhat/source/Quake/bin/jellyfish? Specifically, it should be set executable.

[Medhat]

no i did change it sudo chmod -R 777 jellyfish but the same error

Answer 1

[Medhat]

OK I manage to make the program run but this is not a solution it just work around I used command "--no_jelly" so it worked till I find the solution . the command will be

python quake.py -f /home/medhat/Downloads/genomeList.ls --no_jelly -k 15 -p 2

[mhkt19]

I have a same problem now, did you find finally any solution how to use jellyfish with quake? because it takes lots of time without it to produce the result.